SANTA CLARA, Calif. -- Save for one brief moment in Wednesday's first joint practice between the Denver Broncos and San Francisco 49ers, it was a mostly peaceful day at the office for both sides. But any tension that built up Wednesday boiled over when the teams reconvened for Thursday's practice.

Although 49ers coach Kyle Shanahan and Broncos coach Vance Joseph laid down specific ground rules for the practice sessions, including one asking the teams not to take it beyond the whistle, there were a few skirmishes during Thursday's two-hour practice.

The first and most serious confrontation happened early in practice when the Niners' offense was going against Denver's defense in 7-on-7 red zone drills. Niners quarterback Brian Hoyer threw a pass over the middle for receiver Jeremy Kerley, but Kerley couldn't bring the ball in and it bounced off his hands and into the arms of Denver safety Justin Simmons. As Simmons returned the pick, 49ers wideout Pierre Garcon and Denver cornerback Aqib Talib mixed it up as Kerley and Broncos corner Chris Harris Jr. also were part of a fracas that quickly expanded.

Although there were a few dust-ups, the 49ers' Prince Charles Iworah and the Broncos' Hunter Sharp exchanged pleasantries during this week's joint practices. AP Photo/Marcio Jose Sanchez

Meanwhile, on the other field, the 49ers' defensive line and Broncos' offensive line also mixed it up a couple of times, and there was one more short fight after that. Those battles didn't progress much further, though, and nobody was hurt. Garcon and Talib were seen laughing and joking with each other after the practice.

"It was definitely dirty but they squashed it, everything is good and we'll be ready to roll on Saturday," Harris said. "It's the joint practices. That's why I don't like them really. Things like that happen, anybody can get hurt doing something stupid like that. That's the reason I like being at home practicing with our guys."

Interesting enough, the Niners seemed to be the ones willing to open the door to some of the issues and didn't allow the Broncos to push them around, as they did a year ago in joint practice sessions in Denver. While Shanahan would prefer to avoid the fights, he said much can be learned about his team from some of those situations so long as they don't escalate too far.

"It’s really important to me to see us compete and have each other’s back and not turn anything down," Shanahan said. "That’s very important. You want to know about everybody. When you get in some of those situations, you can really see how people are and how they respond. I think it’s a very hard thing to be that competitive, that physical, in this sport especially, and to play that aggressive between the whistles and stuff, and then when something does happen, not to lose your cool. Because you’ve got to go to a different state to just get to that level to compete in the sport. I think it takes practice and I think it takes a special person to play that violent of a game. But never to really lose your reality.”

Aside from the dustups, both teams believe the past two days were beneficial, and it's logical to think this is an arrangement that will continue as the Broncos and Niners have had joint practices in each of the past three years.

Some other news, notes and observations from Thursday's practice:

-- Linebacker NaVorro Bowman suffered what he called a "stinger" in his neck and shoulder during practice and did not return. Bowman said the injury is minor and common, and he could have returned had the Niners' medical staff allowed him.

More people play on ESPN than anywhere else. Join or create a league in the No. 1 Fantasy Football game! Sign up for free!

-- The Niners' offense once again held its own against Denver's defense. To my eye, Hoyer was sharper Thursday than Wednesday and was able to get the ball down the field with a bit more success this time. He and Victor Bolden Jr. had a couple of nice completions, including one on a deep ball down the sideline and another over the middle in 7-on-7 that would have gone for a big gain. The Niners were particularly effective in 7-on-7 with only a couple of incompletions in the first period.

-- On the other field, the Niners' defense got a much stiffer test from Denver's offense on Thursday. Broncos quarterback Paxton Lynch was much better than he was Wednesday, and a banged-up 49ers defense spent a lot of the practice mixing and matching. Cornerback K'Waun Williams had a nice pass breakup in team drills and defensive tackle Chris Jones was stout against the run, but the Broncos beat Niners corner Keith Reaser for a big play and were far more consistent than Wednesday.

-- Another thing on Bowman, who was rumored to be facing potential discipline from the league back in the spring for his participation in an arm wrestling tournament with other players: Bowman confirmed he has not faced any discipline yet from the league though the NFL says the case is still open and theoretically could do something. Bowman won $50,000, which he is donating to charity, and a trophy for claiming victory in his weight class.

-- Shanahan said rookie quarterback C.J. Beathard will get the first opportunity to replace Brian Hoyer and work with the No. 2 offense against the Broncos on Saturday night. Beathard could play into the third quarter, according to Shanahan. Matt Barkley, who was second last week, will follow Hoyer and Beathard.

-- As for the rest of the starters, Shanahan said he'd like to see them get more time this week than last week, with the goal to get them about 20 snaps apiece.

-- Former United States secretary of state Condoleezza Rice took in Thursday's practice and chatted briefly with Niners general manager John Lynch and Broncos general manager John Elway. Lynch and Elway are Stanford alums. Rice has spent time working there.

-- Thursday's practice was the final one of the "training camp" portion of this preseason. According to Shanahan, not much changes from here.

“It’s weird, especially when you don’t go away [to camp]," Shanahan said. "Every day is kind of the same day. I got reminded right at the end that tonight guys aren’t staying in the hotel and things like that. We’re going to be in the same time tomorrow, at the same place."